RchiOBHm_Chr3g0457091

transposition, RNA-mediated

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_chinensis
3
OG0000094
Physical Location & Seq
Reverse (-)
6325485 .. 6326553
1069 bp
Loading structure...
UTR
Exon/CDS
Intron
PRQ42385

Sequence Viewer

Length: 1029 bp
ATGAACAGGGTGTTTCGCCTGTATCTTGACCGCTTTGTGATTGTGTTCATTGACGACATATTGGTTTATTCTAAGAGTGAGGAGTTACATGTTAAGCACTTGAATATTGTGTTGGAGACTCTACGGCTACACCAATTGTATGCTAAATTCAGTAAGTGTGAGTTTTGGCTTGACCAAGTAACATTCTTGGGTCACGTCATTACAGCTGGTGGTGTTAGTGTGGATCCCCAAAAGGTAGAAGCCGTGTTGAATTGGGAAAGACCTACCAATGTGACGGAAATTCGTAGTTTCTTGGGTCTTGCTGGTTATTATCGACGTTTTGTGCAAAACTTTTCTAGAATTGCCGCTCCTCTTACTAAGTTAACGAGAAAGGGTGTCAGATTTGTTTGGTCTGAGAATTGTGAGCAGAGCTTTCAAGAACTTAAGAGTCGGCTGACTAGTGCTCCAATTTTATCTTTGCCTGATGATAGTGGGGAGTATGTAATTTACAGCGATGCCTCTAGACAAGGCTTAGGCTGTGTTCTAATGCAACATGGTAATGTGATTGCTTATGCTTCTAGACAGTTGAAGCCACATGAGTTGAATTATCCCACACATGACTTAGAATTGGCAGCTATTGTACTTGCTCTTAAGTTGTGGAGGCATTATCTGTATGGAGCCAGATGTCAGATCTTCACTGACCATAAAAGCCTCAAGTATGTGTTTACACAACCGAATTTAAATTTAAGACAACGAAGATGGATGGAGTTGATTGAAGATTATGATTGTACCATTGAGTACCACCCCGGTAAAGCAAATGTGGTGGCGGATGCACTTAGTAGGAACCCATCTGTGACTTTGTCATATTTAAGGGCCACTCGAGTACCCCTATTGTCAGAGTTGAGGTCTACGGGGGTTGAGTTATCGGTTGATGAGGTTGGTACTCTGGTGGCTAGTTTTCATGTGAGACCAGCATTCATTGATAAAATACGGGAAAACCAGCCTCTTGATCCAAGAATTGAAGGGATTAAAGAAGGTATGGGACATTGA
Functional Annotation
Gene Ontology
Molecular Function
Biological Process
Cellular Component
No ontology terms assigned.
KEGG Pathways
Metabolic & Signaling
No pathways identified.
Pfam Domains
Protein Families
RVP_2 RVT_1 Retrotrans_gag rve zf-CCHC

Protein Analysis

342

Amino Acids

39.35

Weight (kDa)

8.49

Isoelectric Point (pI)

41.03

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
RVT_1 PF00078 1 - 67 9.6e-12 Reverse transcriptase (RNA-dependent DNA polymerase)
RT_RNaseH_2 PF17919 130 - 223 1.7e-31 RNase H-like domain found in reverse transcriptase
RT_RNaseH PF17917 156 - 254 5.4e-32 RNase H-like domain found in reverse transcriptase
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter
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Publication-ready
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Orthologous Genes (Group: OG0000094)

Species Orthologous Gene IDs
arabidopsis_thaliana AT1G42190
fragaria_vesca FvH4_1g22371 FvH4_1g23261 FvH4_1g27933 FvH4_1g27934 FvH4_1g29231 FvH4_2g02781 FvH4_2g08031 FvH4_2g08581 FvH4_3g06961 FvH4_3g06962 FvH4_3g13531 FvH4_3g14391 FvH4_3g14392 FvH4_3g18622 FvH4_3g18964 FvH4_3g26314 FvH4_3g28781 FvH4_3g30771 FvH4_3g30772 FvH4_3g31752 FvH4_3g32803 FvH4_3g35751 FvH4_3g35752 FvH4_4g02151 FvH4_4g02642 FvH4_4g05523 FvH4_4g05524 FvH4_4g06574 FvH4_4g06722 FvH4_4g08644 FvH4_4g08645 FvH4_4g08646 FvH4_4g08851 FvH4_4g08971 FvH4_4g09081 FvH4_4g09243 FvH4_4g09244 FvH4_4g09283 FvH4_4g10021 FvH4_4g10032 FvH4_4g10033 FvH4_4g10182 FvH4_4g10361 FvH4_4g12502 FvH4_4g12503 FvH4_4g13341 FvH4_4g13942 FvH4_4g13943 FvH4_4g13944 FvH4_4g14432 FvH4_4g14822 FvH4_4g14823 FvH4_4g15291 FvH4_4g15292 FvH4_4g15293 FvH4_4g15471 FvH4_4g15583 FvH4_4g15584 FvH4_4g15585 FvH4_4g15586 FvH4_4g15587 FvH4_4g15591 FvH4_4g15592 FvH4_4g15593 FvH4_4g16179 FvH4_4g18131 FvH4_4g21031 FvH4_4g22021 FvH4_4g22021 FvH4_4g22042 FvH4_5g03402 FvH4_5g07411 FvH4_5g13881 FvH4_5g15792 FvH4_5g24682 FvH4_5g24911 FvH4_5g25322 FvH4_5g25641 FvH4_5g36692 FvH4_5g38072 FvH4_5g38171 FvH4_6g05202 FvH4_6g08531 FvH4_6g16342 FvH4_6g21771 FvH4_6g23303 FvH4_6g23961 FvH4_6g25381 FvH4_6g27021 FvH4_6g27022 FvH4_6g30091 FvH4_6g30092 FvH4_7g02051 FvH4_7g06031 FvH4_7g07031 FvH4_7g07581 FvH4_7g08381 FvH4_7g11551 FvH4_7g19711 FvH4_7g25621 FvH4_7g29722
malus_domestica MD06G1134500.v1.1 MD09G1067600.v1.1 MD13G1145500.v1.1 MD15G1166500.v1.1 MD16G1270000.v1.1
prunus_persica Prupe.7G030900_v2.0.a1
pyrus_communis pycom01g00710 pycom01g03760 pycom03g10770 pycom04g02180 pycom05g08050 pycom06g04140 pycom06g11110 pycom07g07550 pycom07g21570 pycom08g17240 pycom09g13900 pycom09g19570 pycom10g22300 pycom11g03210 pycom11g13750 pycom11g24890 pycom12561g00270 pycom12668g00020 pycom12g11280 pycom12g20720 pycom12g20730 pycom13g21410 pycom13g21660 pycom14g06010 pycom14g06370 pycom14g12800 pycom16g21440 pycom16g22530 pycom17g02030 pycom420g00170 pycom50g00020 pycom5153684g00110 pycom520g00860 pycom581g00060
rosa_chinensis RchiOBHm_Chr0c08g0498091 RchiOBHm_Chr0c08g0498101 RchiOBHm_Chr1g0326991 RchiOBHm_Chr2g0084311 RchiOBHm_Chr2g0090701 RchiOBHm_Chr2g0098591 RchiOBHm_Chr2g0109491 RchiOBHm_Chr2g0109501 RchiOBHm_Chr2g0130801 RchiOBHm_Chr2g0145931 RchiOBHm_Chr2g0168091 RchiOBHm_Chr3g0457081 RchiOBHm_Chr3g0457091 RchiOBHm_Chr3g0467781 RchiOBHm_Chr3g0467791 RchiOBHm_Chr3g0493771 RchiOBHm_Chr3g0494051 RchiOBHm_Chr3g0496881 RchiOBHm_Chr4g0401391 RchiOBHm_Chr4g0414861 RchiOBHm_Chr4g0424081 RchiOBHm_Chr5g0009611 RchiOBHm_Chr5g0049881 RchiOBHm_Chr5g0050351 RchiOBHm_Chr5g0053791 RchiOBHm_Chr5g0078031 RchiOBHm_Chr6g0256481 RchiOBHm_Chr6g0271231 RchiOBHm_Chr6g0286381 RchiOBHm_Chr7g0197101 RchiOBHm_Chr7g0221891 RchiOBHm_Chr7g0237801 RchiOBHm_Chr7g0237821
rosa_multiflora Rmu_sc0000509.1_g000034 Rmu_sc0004751.1_g000014 Rmu_sc0008546.1_g000002 Rmu_sc0009320.1_g000003 Rmu_sc0010661.1_g000006 Rmu_sc0029652.1_g000002
rosa_roxburghii Rroxscaffold_10G00433150 Rroxscaffold_15G00447630 Rroxscaffold_26G00447790 Rroxscaffold_29G00441810 Rroxscaffold_32G00442860 Rroxscaffold_33G00439800 Rroxscaffold_34G00443230 Rroxscaffold_3G00220560 Rroxscaffold_3G00227370 Rroxscaffold_3G00239080 Rroxscaffold_3G00239090 Rroxscaffold_3G00273190 Rroxscaffold_4G00323530 Rroxscaffold_4G00326840 Rroxscaffold_57G00443110 Rroxscaffold_5G00338590 Rroxscaffold_5G00347530 Rroxscaffold_68G00446990 Rroxscaffold_76G00448570 Rroxscaffold_90G00448860
rosa_rugosa Rorug06G0233600
rosa_samantha Rh3CG302700 Rh6DG286700
rosa_wichuraiana Rw0G002280 Rw0G004080 Rw0G011830 Rw1G003690 Rw1G008800 Rw1G009130 Rw1G009140 Rw1G009150 Rw1G009160 Rw1G009410 Rw1G009580 Rw1G012770 Rw1G015850 Rw1G026860 Rw2G003780 Rw2G006480 Rw2G016520 Rw2G016960 Rw2G018170 Rw2G025180 Rw2G025510 Rw2G025610 Rw2G025750 Rw2G025920 Rw2G029950 Rw2G046360 Rw2G046370 Rw2G046380 Rw3G009070 Rw3G025820 Rw3G027340 Rw3G027900 Rw3G028150 Rw3G029060 Rw4G002440 Rw4G005960 Rw4G007520 Rw4G011970 Rw4G011980 Rw4G012190 Rw4G012530 Rw4G018490 Rw4G026380 Rw5G003970 Rw5G030920 Rw5G031780 Rw5G031900 Rw5G033030 Rw5G033040 Rw5G036330 Rw5G039730 Rw5G048110 Rw6G006670 Rw6G007910 Rw6G009720 Rw6G010990 Rw6G012930 Rw6G012940 Rw6G013420 Rw6G014690 Rw6G015290 Rw6G015790 Rw6G015920 Rw6G036510 Rw7G016650 Rw7G023140 Rw7G028650 Rw7G036450 Rw7G036460 Rw7G036910

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AccBSI CCGCTC 1 cut(s) 347
AccI GTMKAC 1 cut(s) 887
AciI CCGC 3 cut(s) 31, 345, 806
AclWI GGATC 3 cut(s) 218, 231, 983
AcsI RAATTY 4 cut(s) 146, 279, 715, 721
AfaI GTAC 5 cut(s) 621, 769, 779, 864, 922
AflII CTTAAG 2 cut(s) 422, 629
AflIII ACRYGT 1 cut(s) 88
AgsI TTSAA 7 cut(s) 103, 250, 416, 568, 583, 755, 1001
AhlI ACTAGT 1 cut(s) 437
AjiI CACGTC 1 cut(s) 196
AjuI GAANNNNNNNTTGG 2 cut(s) 95, 127
AluBI AGCT 3 cut(s) 206, 411, 614
AluI AGCT 3 cut(s) 206, 411, 614
Alw21I GWGCWC 1 cut(s) 445
Alw26I GTCTC 2 cut(s) 110, 940
AlwI GGATC 3 cut(s) 218, 231, 983
Ama87I CYCGRG 1 cut(s) 858
AoxI GGCC 1 cut(s) 852
ApeKI GCWGC 1 cut(s) 611
ApoI RAATTY 4 cut(s) 146, 279, 715, 721
AspS9I GGNCC 1 cut(s) 852
AsuC2I CCSGG 1 cut(s) 786
AvaI CYCGRG 1 cut(s) 858
BaeI ACNNNNGTAYC 4 cut(s) 846, 879, 912, 945
BamHI GGATCC 1 cut(s) 223
Bbv12I GWGCWC 1 cut(s) 445
BbvI GCAGC 1 cut(s) 623
BccI CCATC 3 cut(s) 732, 736, 835
BceAI ACGGC 2 cut(s) 140, 227
BcnI CCSGG 1 cut(s) 786
BcoDI GTCTC 2 cut(s) 110, 940
BcuI ACTAGT 1 cut(s) 437
BfaI CTAG 5 cut(s) 336, 438, 501, 558, 933
BfrI CTTAAG 2 cut(s) 422, 629
BglII AGATCT 1 cut(s) 669
BisI GCNGC 2 cut(s) 345, 612
BlsI GCNGC 2 cut(s) 346, 613
Bme1390I CCNGG 1 cut(s) 786
BmeT110I CYCGRG 1 cut(s) 858
BmgBI CACGTC 1 cut(s) 196
BmgT120I GGNCC 1 cut(s) 852
BmiI GGNNCC 3 cut(s) 225, 658, 824
BmrFI CCNGG 1 cut(s) 786
BmsI GCATC 2 cut(s) 484, 799
Bpu10I CCTNAGC 1 cut(s) 511
BpuEI CTTGAG 1 cut(s) 677
BpuMI CCSGG 1 cut(s) 786
BsaI GGTCTC 1 cut(s) 940
BsaJI CCNNGG 1 cut(s) 784
BsaXI ACNNNNNCTCC 2 cut(s) 427, 457
BseDI CCNNGG 1 cut(s) 784
BseGI GGATG 2 cut(s) 747, 814
BseMII CTCAG 1 cut(s) 384
BseRI GAGGAG 2 cut(s) 95, 339
BseXI GCAGC 1 cut(s) 623
BshFI GGCC 1 cut(s) 854
BsiHKAI GWGCWC 1 cut(s) 445
BsiHKCI CYCGRG 1 cut(s) 858
BsiSI CCGG 1 cut(s) 786
BsmAI GTCTC 2 cut(s) 110, 940
BsmI GAATGC 1 cut(s) 953
BsnI GGCC 1 cut(s) 854
Bso31I GGTCTC 1 cut(s) 940
BsoBI CYCGRG 1 cut(s) 858
Bsp1286I GDGCHC 1 cut(s) 445
Bsp143I GATC 3 cut(s) 223, 669, 988
BspACI CCGC 3 cut(s) 31, 345, 806
BspANI GGCC 1 cut(s) 854
BspCNI CTCAG 1 cut(s) 385
BspLI GGNNCC 3 cut(s) 225, 658, 824
BspPI GGATC 3 cut(s) 218, 231, 983
BspTI CTTAAG 2 cut(s) 422, 629
BspTNI GGTCTC 1 cut(s) 940
BsrBI CCGCTC 1 cut(s) 347
BssECI CCNNGG 1 cut(s) 784
BssMI GATC 3 cut(s) 223, 669, 988
Bst4CI ACNGT 1 cut(s) 564
BstAFI CTTAAG 2 cut(s) 422, 629
BstDEI CTNAG 6 cut(s) 72, 357, 393, 511, 601, 815
BstF5I GGATG 2 cut(s) 747, 814
BstKTI GATC 3 cut(s) 226, 672, 991
BstMAI GTCTC 2 cut(s) 110, 940
BstMBI GATC 3 cut(s) 223, 669, 988
BstNSI RCATGY 1 cut(s) 92
BstSCI CCNGG 1 cut(s) 784
BstV1I GCAGC 1 cut(s) 623
BstX2I RGATCY 2 cut(s) 223, 669
BstYI RGATCY 2 cut(s) 223, 669
BsuRI GGCC 1 cut(s) 854
BtgZI GCGATG 1 cut(s) 507
BtrI CACGTC 1 cut(s) 196
BtsCI GGATG 2 cut(s) 747, 814
BtsIMutI CAGTG 1 cut(s) 675
Cfr13I GGNCC 1 cut(s) 852
Csp6I GTAC 5 cut(s) 620, 768, 778, 863, 921
CspCI CAANNNNNGTGG 4 cut(s) 561, 596, 783, 818
CviAII CATG 5 cut(s) 89, 533, 575, 596, 941
CviQI GTAC 5 cut(s) 620, 768, 778, 863, 921
DdeI CTNAG 6 cut(s) 72, 357, 393, 511, 601, 815
DpnI GATC 3 cut(s) 225, 671, 990
DpnII GATC 3 cut(s) 223, 669, 988
DraI TTTAAA 1 cut(s) 720
EciI GGCGGA 1 cut(s) 821
Eco31I GGTCTC 1 cut(s) 940
Eco88I CYCGRG 1 cut(s) 858
FaeI CATG 5 cut(s) 92, 536, 578, 599, 944
FatI CATG 5 cut(s) 88, 532, 574, 595, 940
FblI GTMKAC 1 cut(s) 887
Fnu4HI GCNGC 2 cut(s) 345, 612
FokI GGATG 2 cut(s) 754, 821
Fsp4HI GCNGC 2 cut(s) 345, 612
FspBI CTAG 5 cut(s) 336, 438, 501, 558, 933
GluI GCNGC 2 cut(s) 345, 612
HaeIII GGCC 1 cut(s) 854
HapII CCGG 1 cut(s) 786
Hin1II CATG 5 cut(s) 92, 536, 578, 599, 944
HincII GTYRAC 1 cut(s) 363
HindII GTYRAC 1 cut(s) 363
HinfI GANTC 2 cut(s) 118, 427
HpaI GTTAAC 1 cut(s) 363
HpaII CCGG 1 cut(s) 786
Hpy166II GTNNAC 3 cut(s) 363, 705, 888
Hpy188I TCNGA 4 cut(s) 380, 394, 669, 877
Hpy188III TCNNGA 6 cut(s) 26, 336, 416, 501, 558, 986
Hpy8I GTNNAC 3 cut(s) 363, 705, 888
Hpy99I CGWCG 1 cut(s) 318
HpyAV CCTTC 2 cut(s) 995, 1007
HpyCH4III ACNGT 1 cut(s) 564
HpyCH4IV ACGT 2 cut(s) 195, 316
HpyCH4V TGCA 3 cut(s) 325, 529, 812
HpyF3I CTNAG 6 cut(s) 72, 357, 393, 511, 601, 815
HpySE526I ACGT 2 cut(s) 195, 316
Hsp92II CATG 5 cut(s) 92, 536, 578, 599, 944
KspAI GTTAAC 1 cut(s) 363
Kzo9I GATC 3 cut(s) 223, 669, 988
LmnI GCTCC 3 cut(s) 352, 448, 656
LpnPI CCDG 9 cut(s) 32, 192, 288, 474, 673, 799, 911, 963, 992
Lsp1109I GCAGC 1 cut(s) 623
LweI GCATC 2 cut(s) 484, 799
MaeI CTAG 5 cut(s) 336, 438, 501, 558, 933
MaeII ACGT 2 cut(s) 195, 316
MaeIII GTNAC 5 cut(s) 84, 178, 191, 271, 832
MalI GATC 3 cut(s) 225, 671, 990
MbiI CCGCTC 1 cut(s) 347
MboI GATC 3 cut(s) 223, 669, 988
MboII GAAGA 3 cut(s) 664, 747, 767
MfeI CAATTG 1 cut(s) 134
MflI RGATCY 2 cut(s) 223, 669
MhlI GDGCHC 1 cut(s) 445
MlyI GAGTC 2 cut(s) 112, 436
MmeI TCCRAC 1 cut(s) 93
MnlI CCTC 8 cut(s) 73, 360, 508, 633, 701, 876, 907, 993
MseI TTAA 8 cut(s) 93, 362, 423, 630, 719, 725, 848, 1008
MslI CAYNNNNRTG 1 cut(s) 537
MspA1I CMGCKG 1 cut(s) 206
MspCI CTTAAG 2 cut(s) 422, 629
MspI CCGG 1 cut(s) 786
MspR9I CCNGG 1 cut(s) 786
MunI CAATTG 1 cut(s) 134
Mva1269I GAATGC 1 cut(s) 953
NciI CCSGG 1 cut(s) 786
NdeII GATC 3 cut(s) 223, 669, 988
NlaIII CATG 5 cut(s) 92, 536, 578, 599, 944
NlaIV GGNNCC 3 cut(s) 225, 658, 824
NmuCI GTSAC 3 cut(s) 191, 271, 832
NspI RCATGY 1 cut(s) 92
PaeR7I CTCGAG 1 cut(s) 858
PciI ACATGT 1 cut(s) 88
PctI GAATGC 1 cut(s) 953
PflFI GACNNNGTC 1 cut(s) 838
PkrI GCNGC 2 cut(s) 346, 613
PleI GAGTC 2 cut(s) 112, 435
PpsI GAGTC 2 cut(s) 112, 435
PscI ACATGT 1 cut(s) 88
PspN4I GGNNCC 3 cut(s) 225, 658, 824
PspPI GGNCC 1 cut(s) 852
PspXI VCTCGAGB 1 cut(s) 858
PsuI RGATCY 2 cut(s) 223, 669
PsyI GACNNNGTC 1 cut(s) 838
PvuII CAGCTG 1 cut(s) 206
RsaI GTAC 5 cut(s) 621, 769, 779, 864, 922
RsaNI GTAC 5 cut(s) 620, 768, 778, 863, 921
RseI CAYNNNNRTG 1 cut(s) 537
SaqAI TTAA 8 cut(s) 93, 362, 423, 630, 719, 725, 848, 1008
SatI GCNGC 2 cut(s) 345, 612
Sau3AI GATC 3 cut(s) 223, 669, 988
Sau96I GGNCC 1 cut(s) 852
SchI GAGTC 2 cut(s) 112, 436
ScrFI CCNGG 1 cut(s) 786
SduI GDGCHC 1 cut(s) 445
SfaNI GCATC 2 cut(s) 484, 799
Sfr274I CTCGAG 1 cut(s) 858
SlaI CTCGAG 1 cut(s) 858
SmiI ATTTAAAT 1 cut(s) 720
SmiMI CAYNNNNRTG 1 cut(s) 537
SmlI CTYRAG 4 cut(s) 422, 629, 692, 858
SmoI CTYRAG 4 cut(s) 422, 629, 692, 858
SpeI ACTAGT 1 cut(s) 437
SsiI CCGC 3 cut(s) 31, 345, 806
SspI AATATT 1 cut(s) 106
SspMI CTAG 5 cut(s) 336, 438, 501, 558, 933
StyD4I CCNGG 1 cut(s) 784
SwaI ATTTAAAT 1 cut(s) 720
TaaI ACNGT 1 cut(s) 564
TaiI ACGT 2 cut(s) 198, 319
TaqI TCGA 2 cut(s) 313, 859
TatI WGTACW 1 cut(s) 619
TauI GCSGC 1 cut(s) 347
Tru1I TTAA 8 cut(s) 93, 362, 423, 630, 719, 725, 848, 1008
Tru9I TTAA 8 cut(s) 93, 362, 423, 630, 719, 725, 848, 1008
TscAI CASTG 1 cut(s) 682
TseFI GTSAC 3 cut(s) 191, 271, 832
TseI GCWGC 1 cut(s) 611
Tsp45I GTSAC 3 cut(s) 191, 271, 832
TspDTI ATGAA 4 cut(s) 17, 37, 929, 946
TspGWI ACGGA 1 cut(s) 290
TspRI CASTG 1 cut(s) 682
Tth111I GACNNNGTC 1 cut(s) 838
Vha464I CTTAAG 2 cut(s) 422, 629
XapI RAATTY 4 cut(s) 146, 279, 715, 721
XbaI TCTAGA 3 cut(s) 335, 500, 557
XceI RCATGY 1 cut(s) 92
XhoI CTCGAG 1 cut(s) 858
XmiI GTMKAC 1 cut(s) 887
XspI CTAG 5 cut(s) 336, 438, 501, 558, 933
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.